Quickstart¶
[1]:
import numpy as np
import matplotlib.pyplot as plt
import ipyvasp as ipv
Transform POSCAR¶
Let’s create some dummy POSCAR.
[2]:
poscar = ipv.POSCAR.new(
[[0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5]],
{"Ga": [[0.0, 0.0, 0.0]],"As": [[0.25, 0.25, 0.25]]},
scale = 5
)
site_kws = dict(alpha=1)
ax1, ax2, ax3 = ipv.get_axes((8,3),ncols=3, axes_3d=[0,1,2])
poscar.splot_lattice( ax = ax1, fill = False,label='original',
site_kws=site_kws)
_ = poscar.transform(lambda a,b,c: (b+c-a, a+c-b, a+b-c)).transpose([1,2,0]) # bring a1 to x
print(poscar.last.data.metadata.TM)
poscar.last.splot_lattice( # .last points to last created POSCAR in transform
ax=ax2, fill = False, color='red', label='transformed',
site_kws=site_kws
)
poscar.last.splot_plane([1,1,0],1/2,ax=ax2)
poscar.transform(lambda a,b,c: (a-c,b-c,a+b+c)
).set_zdir([0,0,1]).splot_lattice(ax=ax3,color='red')
print(poscar.last.data.metadata.TM)
ax1.view_init(azim=-25, elev=15)
ax2.view_init(azim=-35, elev=15)
[[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]]
[[ 0.66666667 -0.33333333 0.33333333]
[-0.33333333 0.66666667 0.33333333]
[-0.33333333 -0.33333333 0.33333333]]
<Figure size 1152x432 with 0 Axes>
[3]:
poscar.splot_bz(fill = True,color='skyblue', vectors=None,lw=0.1).set_axis_off()
ax = poscar.splot_kpath([(0,0,0), (1/4,1/2,-1/4), (0.5,0.5,0), (0,0,0), (0,0.5,0)],
labels = ['Γ', 'K', 'X', 'Γ', 'L'], fmt_label=lambda lab: lab+'\n')
ax.view_init(azim=55, elev=25)
<Figure size 489.6x489.6 with 0 Axes>
[4]:
fig = poscar.iplot_bz(color='blue')
ipv.iplot2html(fig)
[4]:
K-Path¶
We can interplate kpath based on current POSCAR, it gives correct distance between points.
[5]:
poscar.get_kpath([
(0,0,0,'Γ'),
(1/4,1/2,-1/4,'K'),
(0.5,0.5,0,'X'),
(0,0,0,'Γ'),
(0,0.5,0,'L')
], n=8)
Automatically generated using ipyvasp for HSK-PATH 0:Γ, 4:K, 5:X, 9:Γ, 12:L
13
Reciprocal Lattice
0.0000000000 0.0000000000 0.0000000000 0.076923
0.0625000000 0.1250000000 -0.0625000000 0.076923
0.1250000000 0.2500000000 -0.1250000000 0.076923
0.1875000000 0.3750000000 -0.1875000000 0.076923
0.2500000000 0.5000000000 -0.2500000000 0.076923
0.5000000000 0.5000000000 0.0000000000 0.076923
0.3750000000 0.3750000000 0.0000000000 0.076923
0.2500000000 0.2500000000 0.0000000000 0.076923
0.1250000000 0.1250000000 0.0000000000 0.076923
0.0000000000 0.0000000000 0.0000000000 0.076923
0.0000000000 0.1666666667 0.0000000000 0.076923
0.0000000000 0.3333333333 0.0000000000 0.076923
0.0000000000 0.5000000000 0.0000000000 0.076923
[6]:
poscar.get_kmesh(2,2,2, weight=0)
Generated uniform mesh using ipyvasp, GRID-SHAPE = [2,2,2]
8
Reciprocal
0.0000000000 0.0000000000 0.0000000000 0.000000
1.0000000000 0.0000000000 0.0000000000 0.000000
0.0000000000 1.0000000000 0.0000000000 0.000000
1.0000000000 1.0000000000 0.0000000000 0.000000
0.0000000000 0.0000000000 1.0000000000 0.000000
1.0000000000 0.0000000000 1.0000000000 0.000000
0.0000000000 1.0000000000 1.0000000000 0.000000
1.0000000000 1.0000000000 1.0000000000 0.000000
[7]:
view = poscar.view_ngl(color='red', dashboard=True)
view
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ipyvasp/lattice.py:136, in ngl_viewer(poscar, colors, sizes, plot_cell, linewidth, color, bond_color, width, height, plot_vectors, dashboard, origin, eqv_sites)
135 try:
--> 136 import nglview as nv
137 except ImportError:
ModuleNotFoundError: No module named 'nglview'
During handling of the above exception, another exception occurred:
ImportError Traceback (most recent call last)
Cell In[7], line 1
----> 1 view = poscar.view_ngl(color='red', dashboard=True)
2 view
File /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ipyvasp/lattice.py:431, in POSCAR.view_ngl(self, **kwargs)
428 @_sub_doc(ngl_viewer, {"poscar :.*colors :": "colors :"})
429 @_sig_kwargs(ngl_viewer, ("poscar",))
430 def view_ngl(self, **kwargs):
--> 431 return ngl_viewer(self, **kwargs)
File /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ipyvasp/lattice.py:138, in ngl_viewer(poscar, colors, sizes, plot_cell, linewidth, color, bond_color, width, height, plot_vectors, dashboard, origin, eqv_sites)
136 import nglview as nv
137 except ImportError:
--> 138 raise ImportError("Please install nglview to use this function.")
140 # Only show equivalent sites if plotting cell, only shift origin otherwise
141 poscar = POSCAR( # don't change instance itself, make new one
142 data=plat._fix_sites(poscar.data, eqv_sites=eqv_sites, origin=origin)
143 )
ImportError: Please install nglview to use this function.
If you are not seeing interactive widget above, don’t worry! We’ve got you covered with a screenshot below:
[8]:
view.download_image('nglview.png',factor=8, trim=True,)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[8], line 1
----> 1 view.download_image('nglview.png',factor=8, trim=True,)
NameError: name 'view' is not defined
Live View of POSCAR Operations¶
Batch analysis using Files class.¶
[9]:
files = ipv.Files('..')
files
[9]:
Files(
PosixPath('../_autosummary'),
PosixPath('../apidoc.rst'),
PosixPath('../conf.py'),
PosixPath('../examples.rst'),
PosixPath('../index.rst'),
PosixPath('../modules.rst'),
PosixPath('../notebooks'),
PosixPath('../summary.rst')
) 8 items
[10]:
files.summarize(lambda path: {'end': path.parts[-1]})
[10]:
| end | FILE | |
|---|---|---|
| 0 | _autosummary | ../_autosummary |
| 1 | apidoc.rst | ../apidoc.rst |
| 2 | conf.py | ../conf.py |
| 3 | examples.rst | ../examples.rst |
| 4 | index.rst | ../index.rst |
| 5 | modules.rst | ../modules.rst |
| 6 | notebooks | ../notebooks |
| 7 | summary.rst | ../summary.rst |
[11]:
files.map(lambda p: p.suffix,to_df=True)
[11]:
| 0 | 1 | |
|---|---|---|
| 0 | ../_autosummary | |
| 1 | ../apidoc.rst | .rst |
| 2 | ../conf.py | .py |
| 3 | ../examples.rst | .rst |
| 4 | ../index.rst | .rst |
| 5 | ../modules.rst | .rst |
| 6 | ../notebooks | |
| 7 | ../summary.rst | .rst |
[12]:
files.input_info()
Skipping paths that do not exist: ['../POSCAR']
[12]:
[13]:
files.interactive(lambda file: print(file))
[13]:
[14]:
files.filtered('py')
[14]:
Files(
PosixPath('../conf.py')
) 1 items
Example: View Lattice and BZ side by side¶
[15]:
import plotly.graph_objects as go
import ipyvasp as ipv
fs = ipv.Files('<root_path>','**/POSCAR')
@fs.interact(fig1 = go.FigureWidget(), fig2 = go.FigureWidget(),
app_layout={"left_sidebar": ('file', 'fig1'), 'center':('fig2',)})
def view(file, fig1, fig2):
pos = ipv.POSCAR(file)
ipv.iplot2widget(pos.iplot_bz(), fig_widget=fig2)
ipv.iplot2widget(pos.iplot_lattice(), fig_widget=fig1)
